fix docs: add conda install, fix typos, update deps

Author: amkram

README.md

@@ -7,27 +7,26 @@ Given a pangenome (in [PanMAN](https://github.com/TurakhiaLab/panman) format) an
 ### Modes
 
 - **Single-sample** (default): Places reads from a single sample, aligns to the best-matching reference, and genotypes variants (BAM + VCF output).
-- **Metagenomic** (`--meta`): Scores reads from a mixture sample against every node in the PanMAN, and uses the scoring informtion to estimate haplotype abundance or directly assign reads to nodes.
+- **Metagenomic** (`--meta`): Scores reads from a mixture sample against every node in the PanMAN, and uses the scoring information to estimate haplotype abundance or directly assign reads to nodes.
 
 
 
-### Installation with Docker (recommended)
+### Installation
 
-**Docker build**
+**Bioconda (recommended)**
 
 ```bash
-docker build -t panmap .
-docker run --rm panmap panmap -h
+conda install -c bioconda panmap
 ```
 
-**Docker pull**
+**Docker**
 
 ```bash
-docker pull alanalohaucsc/panmap:latest
+docker build -t panmap .
 docker run --rm panmap panmap -h
 ```
 
-See below for building from source.
+See the [documentation](https://amkram.github.io/panmap/) for building from source.
 
 ## Usage
 
@@ -76,14 +75,20 @@ panmap ref.panman reads_R1.fq reads_R2.fq --stop genotype -t 8 -o sample
 First step is to build an index for metagenomics mode:
 
 ```bash
-make example_run && cd example_run
-../build/bin/panmap ../examples/data/sars_20000_twilight_dipper.panman --index-mgsr sars_20000_twilight_dipper.idx 
+mkdir example_run && cd example_run
+
+panmap ../examples/data/sars_20000_twilight_dipper.panman \
+  --index-mgsr sars_20000_twilight_dipper.idx
 ```
 
 Then run panmap with the `--meta` option:
 
 ```bash
-../build/bin/panmap  ../examples/data/sars_20000_twilight_dipper.panman  ../examples/data/sars20000_5hap_0snp-a_200000_rep0_R1.fastq.gz ../examples/data/sars20000_5hap_0snp-a_200000_rep0_R2.fastq.gz --meta --index sars_20000_twilight_dipper.idx   --threads 8 --em-delta-threshold 0.00001
+panmap ../examples/data/sars_20000_twilight_dipper.panman \
+  ../examples/data/sars20000_5hap_0snp-a_200000_rep0_R1.fastq.gz \
+  ../examples/data/sars20000_5hap_0snp-a_200000_rep0_R2.fastq.gz \
+  --meta --index sars_20000_twilight_dipper.idx \
+  --threads 8 --em-delta-threshold 0.00001
 ```
 
 Reads used above were simulated shotgun-sequencing reads of SARS-CoV-2 mixtures. For wastewater samples, refer to README
@@ -95,13 +100,20 @@ We first build an index for the vertebrate mitochondrial PanMAN. We recommend us
 
 ```bash
 mkdir example_run && cd example_run
-../build/bin/panmap ../examples/data/v_mtdna.panman --index-mgsr v_mtdna.idx -k 15 -s 8 -l 1
+
+panmap ../examples/data/v_mtdna.panman \
+  --index-mgsr v_mtdna.idx -k 15 -s 8 -l 1
 ```
 
-Then we run panmap with the `--filter-and-assign` option to filter and assign reads to the PanMAN.
+Then run panmap with the `--filter-and-assign` option:
 
 ```bash
-../build/bin/panmap ../examples/data/v_mtdna.panman ../examples/data/subsampled.fastq.gz --meta -i v_mtdna.idx --filter-and-assign --discard 0.6 --dust 5 --taxonomic-metadata ../examples/data/v_mtdna.meta.tsv -t 4 --breadth-ratio --output subsampled
+panmap ../examples/data/v_mtdna.panman \
+  ../examples/data/subsampled.fastq.gz \
+  --meta -i v_mtdna.idx \
+  --filter-and-assign --discard 0.6 --dust 5 \
+  --taxonomic-metadata ../examples/data/v_mtdna.meta.tsv \
+  -t 4 --breadth-ratio --output subsampled
 ```
 
 This outputs 3 files:
@@ -110,18 +122,8 @@ This outputs 3 files:
 
 `.mgsr.assignedReads.out` file containing the number of reads assigned to each node and the indices of the reads assigned, with respect to the the `.mgsr.assignedReads.fastq` file
 
-`.mgsr.assignedReadsLCANode.out` file containg the number of reads assigned to the LCA node and the indices of the reads assigned. *As reads may be assigned to multiple nodes, the LCA node of a read if the LCA of all the nodes it was assigned to.*
-
-### Advanced
+`.mgsr.assignedReadsLCANode.out` file containing the number of reads assigned to the LCA node and the indices of the reads assigned. *As reads may be assigned to multiple nodes, the LCA node of a read is the LCA of all the nodes it was assigned to.*
 
-#### Building from source:
-Dependencies:
+### Building from source
 
-- `CMake >= 3.12`
-- `C++17 compiler`
-- `Protobuf (protobuf-compiler, libprotobuf-dev)`
-- `Boost (program_options, iostreams, filesystem, system, date_time)`
-- `zlib`
-- `Cap'n Proto (capnproto, libcapnp-dev)`
-- `Eigen3 (libeigen3-dev)`
-- `htslib 1.20`
+See the [installation docs](https://amkram.github.io/panmap/installation/) for dependencies and build instructions.

docs/index.md

@@ -16,7 +16,7 @@ panmap takes sequencing reads and a pangenome in [PanMAN](https://github.com/Tur
 
 ```bash
 # Install
-docker build -t panmap .
+conda install -c bioconda panmap
 
 # Place reads (stops after placement by default)
 panmap ref.panman reads_R1.fq reads_R2.fq -t 8 -o sample

docs/installation.md

@@ -1,19 +1,22 @@
 # Installation
 
-## Docker (recommended)
+## Bioconda (recommended)
 
 ```bash
-docker build -t panmap .
+conda install -c bioconda panmap
 ```
 
-Verify:
+This installs `panmap` and `panmanUtils`.
+
+---
+
+## Docker
 
 ```bash
-docker run panmap panmap -h
+docker build -t panmap .
+docker run --rm panmap panmap -h
 ```
 
-Docker bundles all dependencies -- no manual setup required.
-
 ---
 
 ## Building from source
@@ -27,9 +30,9 @@ Docker bundles all dependencies -- no manual setup required.
 | Protobuf | `protobuf-compiler`, `libprotobuf-dev` |
 | Boost | `libboost-program-options-dev`, `libboost-iostreams-dev`, `libboost-filesystem-dev`, `libboost-system-dev`, `libboost-date-time-dev` |
 | zlib | `zlib1g-dev` |
+| htslib | `libhts-dev` |
 | Cap'n Proto | `capnproto`, `libcapnp-dev` |
 | Eigen3 | `libeigen3-dev` |
-| htslib 1.20 | (bundled) |
 
 ### Build
 
@@ -40,6 +43,3 @@ make -j$(nproc)
 ```
 
 The binary is at `build/bin/panmap`.
-
-!!! tip
-    If you hit dependency issues, the Docker build is the fastest path forward.

docs/metagenomic.md

@@ -55,7 +55,7 @@ panmap ../examples/data/sars_20000_twilight_dipper.panman \
   --index sars_20000_twilight_dipper.idx \
   --amplicon-depth SRR19707934.amplicon_stacks.tsv \
   --mask-reads-relative-frequency 0.01 \
-  em-delta-threshold 0.00001 \
+  --em-delta-threshold 0.00001 \
   --output SRR19707934 -t 8
 ```